Variant report

Variant	rs3806914
Chromosome Location	chr5:115912496-115912497
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr5:115912171-115913036	H1-hESC	embryonic stem cell:	n/a	n/a
2	CREB1	chr5:115912213-115913459	GM12878	blood:	n/a	n/a
3	IKZF1	chr5:115912479-115913395	GM12878	blood:	n/a	n/a
4	EP300	chr5:115912408-115913440	GM12878	blood:	n/a	n/a
5	MXI1	chr5:115912432-115913371	GM12878	blood:	n/a	n/a
6	STAT5A	chr5:115911642-115912499	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:115911135-115912558	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F6	chr5:115911652-115912554	H1-hESC	embryonic stem cell:	n/a	chr5:115912374-115912383 chr5:115912021-115912031 chr5:115912093-115912100 chr5:115911997-115912006 chr5:115912093-115912100 chr5:115912093-115912100
9	EP300	chr5:115911664-115913404	GM12878	blood:	n/a	n/a
10	BRCA1	chr5:115911336-115912586	H1-hESC	embryonic stem cell:	n/a	n/a
11	CHD2	chr5:115911292-115913493	GM12878	blood:	n/a	n/a
12	RAD21	chr5:115907512-115912646	SK-N-SH	brain:	n/a	chr5:115907841-115907850 chr5:115911934-115911953 chr5:115907716-115907735 chr5:115908547-115908561
13	MAZ	chr5:115911249-115913425	GM12878	blood:	n/a	chr5:115912792-115912807 chr5:115912793-115912802 chr5:115912792-115912805 chr5:115912794-115912804 chr5:115911492-115911502 chr5:115912794-115912803 chr5:115912792-115912805 chr5:115912794-115912803 chr5:115912793-115912804 chr5:115912792-115912805 chr5:115912790-115912805 chr5:115912792-115912805 chr5:115912793-115912804 chr5:115912793-115912803
14	RAD21	chr5:115911613-115913432	GM12878	blood:	n/a	chr5:115911934-115911953
15	EBF1	chr5:115910383-115913484	GM12878	blood:	n/a	chr5:115912875-115912886 chr5:115912878-115912887
16	RCOR1	chr5:115911602-115913462	GM12878	blood:	n/a	n/a
17	RAD21	chr5:115911297-115912555	H1-hESC	embryonic stem cell:	n/a	chr5:115911934-115911953
18	MTA3	chr5:115911889-115913511	GM12878	blood:	n/a	n/a
19	STAT3	chr5:115912468-115913323	GM12878	blood:	n/a	chr5:115913041-115913052
20	POLR2A	chr5:115910283-115913382	GM12878	blood:	n/a	n/a
21	ATF2	chr5:115912396-115913473	GM12878	blood:	n/a	chr5:115913109-115913120
22	CHD1	chr5:115910361-115913446	GM12878	blood:	n/a	n/a
23	FOXM1	chr5:115911651-115913474	GM12878	blood:	n/a	n/a
24	PML	chr5:115911514-115913522	GM12878	blood:	n/a	n/a
25	CTCF	chr5:115910310-115912531	GM12878	blood:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
26	TBP	chr5:115911752-115913404	GM12878	blood:	n/a	n/a
27	SMC3	chr5:115907633-115912597	SK-N-SH	brain:	n/a	chr5:115908994-115909004 chr5:115907717-115907731 chr5:115911939-115911949 chr5:115909229-115909236
28	SMC3	chr5:115910369-115913364	GM12878	blood:	n/a	chr5:115911939-115911949
29	ATF2	chr5:115912228-115913501	GM12878	blood:	n/a	chr5:115913109-115913120
30	RELA	chr5:115911765-115913404	GM18951	blood:	n/a	n/a
31	CUX1	chr5:115912437-115913386	GM12878	blood:	n/a	n/a
32	TBL1XR1	chr5:115911155-115913346	GM12878	blood:	n/a	n/a
33	CTCF	chr5:115911027-115912516	SK-N-SH	brain:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
34	NFIC	chr5:115912156-115913493	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:115904366..115906105-chr5:115910810..115912566,2	K562	blood:
2	chr5:115911257..115912668-chr5:116283296..116284268,6	MCF-7	breast:
3	chr19:10764160..10766526-chr5:115912031..115913531,2	K562	blood:

Variant related genes	Relation type
SEMA6A	TF binding region
ENSG00000129351	Chromatin interaction
ENSG00000267100	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10045872	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10046086	0.93[EUR][1000 genomes]
rs10053792	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10061055	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10062998	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10066922	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10070276	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10073289	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10074788	0.96[ASN][1000 genomes]
rs10075410	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10080023	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1027742	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs11953558	0.99[ASN][1000 genomes]
rs12719220	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13354122	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13355655	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13357599	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13360587	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1345706	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1345707	0.90[ASN][1000 genomes]
rs17140120	0.93[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17140171	0.93[ASN][1000 genomes]
rs17140176	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17140201	0.88[EUR][1000 genomes]
rs1862372	0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1862373	0.84[ASN][1000 genomes]
rs2840113	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs28489253	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806915	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806916	0.98[ASN][1000 genomes]
rs56257700	0.83[ASN][1000 genomes]
rs57497884	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57557217	0.96[ASN][1000 genomes]
rs58364462	0.92[ASN][1000 genomes]
rs59351578	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6878936	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897765	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6898172	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73780374	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73780375	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9327010	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9327011	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9327012	0.95[ASN][1000 genomes]

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115906800-115912600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:115906800-115912800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:115907200-115912600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:115907200-115912600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr5:115907400-115912600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:115907400-115912600	Active TSS	Brain Angular Gyrus	brain
7	chr5:115907600-115912600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:115907600-115912600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:115907600-115912600	Active TSS	Brain Anterior Caudate	brain
10	chr5:115907600-115912600	Active TSS	Brain Cingulate Gyrus	brain
11	chr5:115907600-115912600	Active TSS	Brain Substantia Nigra	brain
12	chr5:115907800-115912600	Active TSS	Fetal Kidney	kidney
13	chr5:115908000-115912600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:115908200-115912800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr5:115908400-115912600	Active TSS	H9 Cell Line	embryonic stem cell
16	chr5:115909200-115912600	Active TSS	Right Atrium	heart
17	chr5:115909400-115912800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr5:115909800-115912600	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr5:115909800-115912600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr5:115910600-115913000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
21	chr5:115911000-115913000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
22	chr5:115911800-115912600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:115911800-115912600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:115911800-115912600	Active TSS	Brain Hippocampus Middle	brain
25	chr5:115911800-115912600	Active TSS	Duodenum Mucosa	Duodenum
26	chr5:115911800-115913000	Active TSS	Colonic Mucosa	Colon
27	chr5:115911800-115914400	Weak transcription	HepG2	liver
28	chr5:115912000-115912600	Bivalent/Poised TSS	HUVEC	blood vessel
29	chr5:115912000-115912600	Bivalent/Poised TSS	NHEK	skin
30	chr5:115912000-115913000	Enhancers	Fetal Brain Male	brain
31	chr5:115912200-115912600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
32	chr5:115912200-115912600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:115912200-115912600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr5:115912200-115912600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:115912200-115912600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr5:115912200-115912600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
37	chr5:115912200-115912600	Flanking Active TSS	Fetal Muscle Trunk	muscle
38	chr5:115912200-115912800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr5:115912200-115913400	Flanking Active TSS	GM12878-XiMat	blood
40	chr5:115912400-115912600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:115912400-115912600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr5:115912400-115912600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
43	chr5:115912400-115912600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:115912400-115912600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:115912400-115912600	Enhancers	Adipose Nuclei	Adipose
46	chr5:115912400-115912600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr5:115912400-115912600	Flanking Active TSS	Fetal Brain Female	brain
48	chr5:115912400-115912600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
49	chr5:115912400-115912600	Active TSS	Fetal Muscle Leg	muscle
50	chr5:115912400-115912600	Active TSS	Placenta	Placenta

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